Phylogeographic evidence for the existence of an ancient biogeographic barrier: the Isthmus of Kra Seaway

Biogeographic boundaries are characterised by distinct faunal and floral assemblages restricted on either side, but patterns among groups of taxa often vary and may not be discrete. Historical biogeography as a consequence, while providing crucial insights into the relationship between biological diversity and earth history, has some limitations. Patterns of intraspecific molecular variation, however, may show unambiguous evidence for such historical divides, and can be used to test competing biogeographic hypotheses (often based on the dispersal-vicariance debate). Here, we utilise this method to test the hypothesis that a major biogeographic transition zone between the Sundaic and Indochinese biotas, located just north of the Isthmus of Kra in SE Asia, is the result of Neogene marine transgressions that breached the Isthmus in two locations for prolonged periods of time (>1 million year duration). Phylogeographic analyses of a freshwater decapod crustacean, the giant freshwater prawn Macrobrachium rosenbergii, strongly supports the historical existence of the more northerly postulated seaway. Results presented here highlight the power of utilising intraspecific molecular variation in testing biogeographical hypotheses.     

Spatial and temporal variations in calanoid copepod distribution in the Straits of Malacca

The distribution and abundance of planktonic calanoid copepods were studied from samples collected at 13–20 stations during four oceanographic cruises (pre- and post- monsoons, and during northeast (NE) and southwest (SW) monsoons) performed between 1998 and 2000 in the Straits of Malacca. Space and time variations of calanoid copepods were described using univariate (number of species, diversity indices, abundance) as well as multivariate (MDS, ANOSIM, SIMPER) techniques from the Plymouth Routines in Multivariate Ecological Research (PRIMER) package. There were significant differences in abundance between the cruises. k-Dominance curves also revealed significant differences in the relative species abundance distributions among the monsoon periods, and a decrease in diversity from northern to southern parts of the Straits during each cruise. Multi-dimensional scaling revealed four groups of abundances with differences in species composition. Evidence from analysis of similarity (ANOSIM) suggested that the differences in communities among monsoon periods were significant, although spatial differences among samples in geographic locations in the northern, central and southern parts of the Straits were insignificant. These differences resulted from an overall change in the balance of relative abundance of few dominant species, rather from changes of many species. Similarity percentage analyses (SIMPER) indicated that the major species contributing to the average dissimilarity between monsoons varied temporally.     

Guanidine hydrochloride denaturation of human serum albumin originates by local unfolding of some stable loops in domain III

Thiamine triphosphate (ThTP) is found in most organisms and may be an intracellular signal molecule produced in response to stress. We have recently cloned the cDNA coding for a highly specific mammalian 25-kDa thiamine triphosphatase. The enzyme was active in all mammalian species studied except pig, although the corresponding mRNA was present. In order to determine whether the very low ThTPase activity in pig tissues is due to the absence of the protein or to a lack of catalytic efficiency, we expressed human and pig ThTPase in E. coli as GST fusion proteins. The purified recombinant pig GST-ThTPase was found to be 2-3 orders of magnitude less active than human GST-ThTPase. Using site-directed mutagenesis, we show that, in particular, the change of Glu85 to lysine is responsible for decreased solubility and catalytic activity of the pig enzyme. Immunohistochemical studies revealed a distribution of the protein in pig brain very similar to the one reported in rodent brain. Thus, our results suggest that a 25-kDa protein homologous to hThTPase but practically devoid of enzyme activity is expressed in pig tissues. This raises the possibility that this protein may play a physiological role other than ThTP hydrolysis.     

Evidence against essential roles for subdomain 1 of actin in actomyosin sliding movements

We have engineered acto-S1chimera proteins carrying the entire actin inserted in loop 2 of the motor domain of Dictyostelium myosin II with 24 or 18 residue-linkers (CP24 and CP18, respectively). These proteins were capable of self-polymerization as well as copolymerization with skeletal actin and exhibited rigor-like structures. The MgATPase rate of CP24-skeletal actin copolymer was 1.06 s(-1), which is slightly less than the V(max) of Dictyostelium S1. Homopolymer filaments of skeletal actin, CP24, and CP18 moved at 4.7+/-0.6, 2.9+/-0.6, and 4.1+/-0.8 microm/s (mean+/-SD), respectively, on coverslips coated with skeletal myosin at 27 degrees C. Statistically thermodynamic considerations suggest that the S1 portion of chimera protein mostly resides on subdomain 1 (SD-1) of the actin portion even in the presence of ATP. This and the fact that filaments of CP18 with shorter linkers moved faster than CP24 filaments suggest that SD-1 might not be as essential as conventionally presumed for actomyosin sliding interactions.     

Roles of curvature and hydrophobic interstice energy in fusion: studies of lipid perturbant effects

We have examined the effects of small amounts (1-4 mol %) of lipids of different molecular shapes, long chain lipids, and hydrocarbon on the kinetics of PEG-mediated fusion of 1,2-dioleoyl-3-sn-phosphatidylcholine/1,2-dioleoyl-3-sn-phosphatidylethanolamine/sphingomyelin/cholesterol (DOPC/DOPE/SM/CH, 35:30:15:30) sonicated vesicles. The effects of these lipid perturbants were different for different steps in the fusion process and varied with the ratio of the cross-sectional areas of headgroup to acyl chain moieties. For lipids with a ratio <1 (negative intrinsic curvature), a decrease in this ratio led to a dramatic increase in the initial rate of vesicle contents mixing but left the initial rate of lipid mixing roughly unchanged. For lipids with ratios >1 (positive intrinsic curvature), the initial rates of both lipid and contents mixing decreased mildly with increasing ratio. In the context of the "stalk model" for fusion, lipid mixing reflects mainly formation of the initial fusion intermediate (stalk), while contents mixing reflects conversion of this intermediate either to a second intermediate or to a fusion pore. Results with positively curved lipids (ganglioside, GM1; lysophosphatidylcholine, LPCs) and negatively curved lipids (dioleoylglycerol, DOG, and 1,2-diphytanoyl-sn-glyvero-3-phosphatidylcholine, DPhPC) can be taken as supportive of the usual interpretation of the stalk model in terms of bending energy, but enhancement of fusion in the presence of long-chain phospholipids, hexadecane, as well as a mixture of GM1 plus hexadecane could not be explained by their curvature alone. We propose that the ability of a lipid perturbant to compensate for lipid packing mismatch, that is, to lower "void" energy, must be taken into account, along with intrinsic curvature, to explain the ability of lipid perturbants to promote pore formation.     

Effect of nitric oxide on H+ -efflux in presence of various nutrients in Candida albicans

In the present study tentative link has been established between H+ -efflux and effect of NO in presence of various nutrients (glucose, 2-deoxy-D-glucose, xylose, proline, glutamic acid and lysine) in C. albicans using sodium nitroprusside (SNP) as a potent source of NO. It was observed that there was a decreasing trend in pH with time, in control, while SNP treated cells showed an initial decline in pH for 10-15 min, followed by an increase in pH up to 30 min. In presence of glucose there was an enhancement in H+ -efflux by 9-fold whereas proline, glutamic acid and lysine showed enhancement by 3, 6 and 1.5-fold respectively. Similar trends in increase in pH after 15 min in SNP treated cells of Candida was observed in presence of all nutrients used. It was demonstrated for the first time that H+ -ATPase of C. albicans was affected by NO.     

Simultaneous methanogenesis and phototrophic bacterial growth in relatively dry sewage sludge under light

Anaerobically digested sewage sludge with a variety of moisture content, namely 81%, 86%, 90% and 98%, were anaerobically cultured at 35 degrees C under light. Phototrophic bacteria grew in the 86% moisture sludge (bacteriochlorophyll a, 0.46 g/L), 90% sludge (bacteriochlorophyll a, 0.36 g/L) and 98% sludge (bacteriochlorophyll a, 0.04 g/L) with methane production. Phototrophic bacteria could not grow in the 81% moisture sludge (bacteriochlorophyll a 0.004 g/L). Phototrophic bacteria could assimilate about 46% of the extracellular ammonium in the 90% moisture sludge. Phototrophic bacteria utilized organic compounds competing with methanogens; therefore, methane yield from the 90% moisture sludge under the light conditions was lower than that under the dark conditions. Phototrophic bacteria could grow in anaerobically digested sludge with relatively low moisture content, and assimilated extracellular ammonium in the sludge. The quality of digested sludge with phototrophic bacterial biomass for fertilizer could be improved compared with that without phototrophic bacterial biomass.     

Suppressed expression of the apoplastic ascorbate oxidase gene increases salt tolerance in tobacco and Arabidopsis plants

Transgenic tobacco plants expressing the ascorbate oxidase (AAO) gene in sense and antisense orientations, and an Arabidopsis mutant in which the T-DNA was inserted into a putative AAO gene, were used to examine the potential roles of AAO for salt-stress tolerance in plants. AAO activities in the transgenic tobacco plants expressing the gene in sense and antisense orientations were, respectively, about 16-fold and 0.2-fold of those in the wild type. Under normal growth conditions, no significant differences in phenotypes were observed, except for a delay in flowering time in the antisense plants. However, at high salinity, the percentage germination, photosynthetic activity, and seed yields were higher in antisense plants, with progressively lower levels in the wild type and the sense plants. The redox state of apoplastic ascorbate in sense plants was very low even under normal growth conditions. Upon salt stress, the redox state of symplastic and apoplastic ascorbate decreased among the three types of plants, but was lowest in the sense plants. The hydrogen peroxide contents in the symplastic and apoplastic spaces were higher in sense plants, progressively lower in the wild type, followed by the antisense plants. The Arabidopsis T-DNA inserted mutant exhibited very low ascorbate oxidase activity, and its phenotype was similar to that of antisense tobacco plants. These results suggest that the suppressed expression of apoplastic AAO under salt-stress conditions leads to a relatively low level of hydrogen peroxide accumulation and a high redox state of symplastic and apoplastic ascorbate which, in turn, permits a higher seed yield.     

Coarse-grained normal mode analysis in structural biology

The realization that experimentally observed functional motions of proteins can be predicted by coarse-grained normal mode analysis has renewed interest in applications to structural biology. Notable applications include the prediction of biologically relevant motions of proteins and supramolecular structures driven by their structure-encoded collective dynamics; the refinement of low-resolution structures, including those determined by cryo-electron microscopy; and the identification of conserved dynamic patterns and mechanically key regions within protein families. Additionally, hybrid methods that couple atomic simulations with deformations derived from coarse-grained normal mode analysis are able to sample collective motions beyond the range of conventional molecular dynamics simulations. Such applications have provided great insight into the underlying principles linking protein structures to their dynamics and their dynamics to their functions.